The repository contains all the material required to reproduce the figures in the article:
Vanderaa, Christophe, and Laurent Gatto. 2023. “Revisiting the Thorny Issue of Missing Values in Single-Cell Proteomics.” arXiv [q-bio.QM]. arXiv. http://arxiv.org/abs/2304.06654.
This image is licensed under a Creative Commons Attribution 4.0 International License.
make_figure[1234].R
: 4 scripts that produce the article's figures, each figure being generated by a separate script.utils.R
: an R script with functions used by the scripts above.install_dependencies.R
: an R script that installs all the required dependency packages.figs/
: folder containing the generated figures.Dockerfile
: the instructions used to build the Docker image.
Each figure is generated in its own script. We garantee long term
reproducibility by relying on Docker
. You must first install
Docker on your local machine. Then, pull the image from the
DockerHub
repository.
docker pull cvanderaa/2023_scp_na_docker
Then clone this repository on your local machine:
git clone [email protected]:UCLouvain-CBIO/2023_scp_na
cd 2023_scp_na/
Start an Rstudio session within a Docker container using:
docker run -e PASSWORD=bioc -p 8787:8787 -v `pwd`:/home/rstudio/ cvanderaa/2023_scp_na_docker:latest
Note you should use %CD%
instead of pwd
when using Windows.
Open your browser and go to http://localhost:8787. The USER is
rstudio
and the password is bioc
. See the DockerHub
repository
for more detailed information on getting started with Docker
.
(I don't think I'll ever have to rebuild the image, but who knows).
Build the image (make sure to cd
in the 2023_scp_na
local repo):
docker build -t cvanderaa/2023_scp_na_docker .
When complete, push the new image to DockerHub:
docker push cvanderaa/2023_scp_na_docker
To reuse the code for publications, please cite:
Vanderaa, Christophe, and Laurent Gatto. 2023. “Revisiting the Thorny Issue of Missing Values in Single-Cell Proteomics.” arXiv [q-bio.QM]. arXiv. http://arxiv.org/abs/2304.06654.
The code is provided under a permissive Artistic 2.0 license.